Drug-induced phospholipidosis (PL) is a storage disorder caused by the formation of phospholipid-drug complexes in lysosomes. Because of the diversity of PL between species, human cell-based assays have been used to predict drug-induced PL in humans. We established three-dimensional (3D) human liver organoids as described previously and investigated their liver characteristics through multiple analyses. Drug-induced PL was initiated in these organoids and in monolayer HepG2 cultures, and cellular changes were systemically examined. Organoids that underwent differentiation showed characteristics of hepatocytes rather than HepG2 cells. The organoids also survived under PL-inducing drug conditions for 48 h and maintained a more stable albumin secretion level than the HepG2 cells. More cytoplasmic vacuoles were observed in organoids and HepG2 cells treated with more potent PL-induced drugs, but to a greater extent in organoids than in HepG2 cells. Lysosome-associated membrane protein 2, a marker of lysosome membranes, showed a stronger immunohistochemical signal in the organoids. PL-distinctive lamellar bodies were observed only in amiodarone-treated organoids by transmission electron microscopy. Human liver organoids are thus more sensitive to drug-induced PL and less affected by cytotoxicity than HepG2 cells. Since PL is a chronic condition, these results indicate that organoids better reflect metabolite-mediated hepatotoxicity in vivo and could be a valuable system for evaluating the phospholipidogenic effects of different compounds during drug development.Int. J. Mol. Sci. 2020, 21, 2982 2 of 18 stages [6]. PL can occur in target organs without organ-related toxicity or physiological consequences [7], however, there are cases in which PL is observed with target organ toxicity [8]. Due to the uncertainty of the toxicological outcome of PL, drug-induced PL discovered in preclinical studies can have a detrimental impact on pharmaceutical development and delay the process. Fatal genetic disorders such as Niemann-Pick disease and Tay-Sachs disease [9,10] associated with PL have been described in humans, as has cell membrane damage leading to cell death. And other hepatic [11,12] cardiac [13,14], renal [15,16] pulmonary [17,18], eye [19], nervous [20], and skin [21] toxicities related to PL are known.Although drug-induced PL can be detected preclinically using in vivo systems such as animal models [3,[22][23][24], these types of studies are expensive, time-consuming, can raise ethical issues, and may not have specific toxicological relevance to humans. It has also been recommended that compounds that can lead to PL in humans should be identified and screened out in the early stages of drug discovery [25]. PL can be observed in any organ in the body, but the lung, liver, kidney, brain, spleen, and other lymphoid tissues are the most commonly involved sites [26]. To identify chemicals that provoke PL in humans, cell-based in vitro assays using various human liver cell types, such as HepG2 cells, HuH7 cells, and human pri...